Biology subjects

Tomaru, Y.

Publications and source records attributed to Tomaru, Y..

4 recordsLinked to original sources

bioRxiv2026

Metatranscriptomic Profiling of Viral Diversity in Aquatic Environments with a Focus on Microalgal Viruses

Freshwater microeukaryotes contribute to aquatic productivity, yet the RNA viruses associated with these communities remain incompletely characterized compared with their marine counterparts. Here, we used metatranscriptomics to profile viral diversity across five Finnish freshwater sites (one river and four lakes) and one coastal marine sample from Hiroshima Bay in the Seto Inland Sea, Japan. We recovered 399 viral operational taxonomic units (vOTUs), of which 285 (71.4%) represented RNA viruses distributed across five viral phyla and putatively associated with fungal, plant or algal, metazoan and bacterial hosts. DNA viruses formed a smaller component of the dataset, including bacteriophage-like vOTUs with transcripts encoding replication, structural, packaging, and lysis proteins. Two vOTUs, which were detected in the Vantaanjoki river sample, were putatively classified within the family Marnaviridae, which comprises RNA viruses that infect protists in marine and freshwater environments. Both vOTUs encoded conserved replication and picornavirus-like capsid domains, and one represented a near-complete dicistronic genome. RNA-dependent RNA polymerase (RdRp) -based phylogeny placed these vOTUs in a strongly supported lineage outside the currently recognized genera within the family Marnaviridae, supporting their provisional assignment to the candidate genus Vandarnavirus proposed here within Marnaviridae. Whole-genome comparisons using the IMG/VR v4 database revealed genetic similarities between the vOTUs representing the candidate Vandarnavirus genus and picorna-like virus sequences from freshwater, wetland, saltmarsh, and estuarine metatranscriptomes. These findings expand the known ecological range of marnavirus-like RNA viruses and identify freshwater habitats as under-sampled reservoirs of microalgae-associated viral sequences.

microbiology↗

bioRxiv2025

Structural diversity and conservation among CRESS-DNA bacilladnaviruses revealed through cryo-EM and computational modelling

Viruses that infect single-celled algae strongly regulate microalgae growth and community composition through cell lysis, enable nutrient recycling in marine ecosystems, and offer valuable insights into early stages of viral evolution. One major group, the Bacilladnaviridae family of single-stranded DNA viruses, infects diatoms in marine environments. Here, we present the capsid structure of Chaetoceros lorenzianus DNA virus (ClorDNAV, Protobacilladnavirus chaelor) determined at 2.2 [A] resolution, thereby expanding the known structural diversity within the Cressdnaviricota phylum. The ClorDNAV capsid protein (CP) contains a conserved jelly-roll fold and a surface-exposed projection domain, with both N- and C-termini oriented toward the capsid interior. A low-resolution reconstruction of the genome revealed a spooled arrangement of the outer DNA layer, similar to that observed in Chaetoceros tenuissimus DNA virus type II (CtenDNAV-II). Structural comparison with CtenDNAV-II revealed five key CP differences: the absence of surface-exposed C-terminal tails in ClorDNAV, the presence of a helical domain, differences in the projection domain conformation, variation in the number of {beta}-strands in the jelly-roll fold, and the lack of ion-attributed densities at subunit interfaces. Together with the genome reconstruction, these findings underscore the importance of experimentally determined structures for understanding viral architecture and evolution. To complement these results, we analyzed AlphaFold3-predicted CPs from all classified Bacilladnaviridae genera. These models confirmed the conservation of the jelly-roll fold across the family while revealing variability in the surface-exposed and terminal regions, likely reflecting host-specific adaptations and genome packaging strategies. Together, the experimental and predicted structures provide a comprehensive view of structural conservation and divergence in Bacilladnaviridae. Furthermore, the results provide additional structural evidence for the evolution of ssDNA Bacilladnaviridae from a noda-like ssRNA virus ancestor and suggest a shared genome organization within Bacilladnaviridae that resembles those observed in viruses with double-stranded genomes.

microbiology↗

bioRxiv2022

A Novel Bacterial Speciation Process Observed in a Symbiotic Marine Population

Incomplete lineage sorting (ILS), where ancestral polymorphisms persist through rapid speciation, is a hallmark of eukaryotic radiations but undocumented in prokaryotes. We report ILS associated speciation in the globally distributed marine bacterium Sulfitobacter, analyzing 74 strains from 16 oceanic regions and 15 ecosystem types. Genomic analysis resolved over ten genetically monomorphic clades sharing near uniform whole genome divergence (average nucleotide identity {approx}95%). However, individual genes and even adjacent nucleotide sites support conflicting phylogenetic relationships among clades. The median length of nearly identical sequence blocks supporting alternative topologies is less than 50 base pairs, far shorter than typical adaptive cassettes. This within gene, site level discordance provides a diagnostic signature of ancestral polymorphism retention following rapid fragmentation, ruling out adaptive gene sweeps. Demographic inference places this radiation on a timescale of tens of millennia, 100 to 1,000 fold faster than eukaryotic ILS, and traces the clades to a hyper polymorphic, highly recombining ancestor. Neutral simulations show that transient mutation surges or population bottlenecks alone can generate this pattern, without adaptive selection or ecological partitioning. By bridging eukaryotic and prokaryotic speciation paradigms, our findings demonstrate that ILS, previously considered exclusive to sexual eukaryotes, can drive rapid, neutral diversification in bacteria, expanding the mechanisms known to generate prokaryotic biodiversity.

microbiology↗

bioRxiv2021

Primordial capsid and spooled ssDNA genome structures penetrate ancestral events of eukaryotic viruses

Marine algae viruses are important for controlling microorganism communities in the marine ecosystem and played fundamental roles during the early events of viral evolution. Here, we have focused on one major group of marine algae viruses, the ssDNA viruses from the Bacilladnaviridae family. We present the capsid structure of the bacilladnavirus, Chaetoceros tenuissimus DNA virus type II (CtenDNAV-II), determined at 2.3 [A] resolution. A structure-based phylogenetic analysis supported the previous theory that bacilladnaviruses have acquired their capsid protein via horizontal gene transfer from a ssRNA virus. The capsid protein contains the widespread virus jelly-roll fold, but has additional unique features; a third {beta}-sheet and a long C-terminal tail. Further, low-resolution reconstructions of the CtenDNAV-II genome revealed a partially spooled structure, an arrangement previously only described for dsRNA and dsDNA viruses. Together, these results exemplify the importance of genetic recombination for the emergence and evolution of ssDNA viruses and provide important insights into the underlying mechanisms that dictate genome organisation.

biophysics↗